diff --git a/build_system/targets/compilation/cpp/__init__.py b/build_system/targets/compilation/cpp/__init__.py
index c7d5f9a0a..6f931f796 100644
--- a/build_system/targets/compilation/cpp/__init__.py
+++ b/build_system/targets/compilation/cpp/__init__.py
@@ -23,7 +23,7 @@
         .depends_on(VENV) \
         .set_runnables(SetupCpp()) \
     .add_phony_target(COMPILE_CPP) \
-        .depends_on(SETUP_CPP) \
+        .depends_on(SETUP_CPP, clean_dependencies=True) \
         .set_runnables(CompileCpp()) \
     .add_build_target(INSTALL_CPP) \
         .depends_on(COMPILE_CPP) \
diff --git a/build_system/targets/compilation/cython/__init__.py b/build_system/targets/compilation/cython/__init__.py
index be7145746..1d3bce4ae 100644
--- a/build_system/targets/compilation/cython/__init__.py
+++ b/build_system/targets/compilation/cython/__init__.py
@@ -23,7 +23,7 @@
         .depends_on(COMPILE_CPP) \
         .set_runnables(SetupCython()) \
     .add_phony_target(COMPILE_CYTHON) \
-        .depends_on(SETUP_CYTHON) \
+        .depends_on(SETUP_CYTHON, clean_dependencies=True) \
         .set_runnables(CompileCython()) \
     .add_build_target(INSTALL_CYTHON) \
         .depends_on(COMPILE_CYTHON) \